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Tools for tweaking stitching parameters
Stichit uses manually chosen stitching parameters to place tiles. This relies upon good alignment between the scan axes and the motion axes. It also requires a precise value for the number of microns per pixel. All of these things should be defined by the microscope producing the data. The values are read by StitchIt at tile load time and stitch time. To assist in setting these values at the microscope, StitchIt provides the function
chessboardStitch and the associated viewer exploreChessBoard. They work roughly like this:% Stitch physical section 2, optical plane 1, channel 1:
>> IM=chessboardStitch([3,1],1); % IM is a structure
% Now visualise this:
>> exploreChessBoard(IM) % (mouse wheel zooms, right-drag to pan )
>> exploreChessBoard(IM,2000) %Again but with a new threshold
% Say we want to rotate the tiles by -0.4 degrees and compare
% that with the original stitching:
>> IM(2) = IM;
% affineMatGen is in BakingTray
>> IM(2).params.affineMat = affineMatGen('rot', -0.4);
>> IM(2) = chessboardStitch([3,1],1,IM(2)); %To use new parameters
% Compare the two stitching results side by
>> exploreChessBoard(IM,2000)
The above can be used to generate comparisons like this: 
Right is before and left is after tweaking.